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Genetically improved BarraCUDA

Langdon, WB; Lam, BYH; (2017) Genetically improved BarraCUDA. BioData Mining , 10 , Article 28. 10.1186/s13040-017-0149-1. Green open access

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Abstract

Background: BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using “Genetic Improvement”. Results: The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. Conclusions: The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.

Type: Article
Title: Genetically improved BarraCUDA
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s13040-017-0149-1
Publisher version: http://dx.doi.org/10.1186/s13040-017-0149-1
Language: English
Additional information: Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords: Science & Technology, Life Sciences & Biomedicine, Mathematical & Computational Biology, GPGPU, Parallel computing, Genetic improvement, Double-ended DNA sequence, Nextgen NGS, LONG-READ ALIGNMENT, ACCURATE, SOFTWARE
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: http://discovery.ucl.ac.uk/id/eprint/1526401
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